Porous bioceramic scaffolds are the preferred option for substituting spongy bone. Therefore, this study evaluates the use of carbonate associated with apatite rocks at Hamadat mines (referred to as calcite) as a source of low-cost bioactive material useful for biomedical applications. In this study, the depositional environment and mineralogical, and petrographic behavior of such depositions were studied. Furthermore, the possibility of producing highly porous, low-cost bioceramic scaffolds using the freeze-drying technique was demonstrated. The bioactivity of the produced scaffolds was enhanced by adding different ratios of wollastonite (25, 50 and 75 wt %) to the scaffold’s batches. However, the scaffolds were coated with ZnCl2 to enhance their antimicrobial susceptibility. The physical and mechanical properties as well as the phase composition and microstructure of the prepared scaffolds were investigated. The X-ray diffraction results revealed the formation of pure phase of α-wollastonite after 3 h of sintering at 1200 °C. To estimate the scaffolds’ biodegradability, the pH and the weight change were measured. The results were confirmed using the inductively coupled plasma measurements for the scaffolds deposited in a simulated body fluid (SBF) solution for 28 days. Results showed that the scaffolds had excellent bioactivity, which was demonstrated by the appearance of apatite particles on their surface after being immersed in the SBF. The antimicrobial activity test revealed that Zn2+, NPs and CaSiO3 had positive effects due to their oxidative stress process. Zn2+, Ca2+, and Si4+ cations can be adsorbed on bacterial surface membranes, interacting with the respiratory microbial enzymes, inhibiting their actions, and damaging the cell, thereby causing the bacterial cell decomposition.